Actually, there should be no problem with the saves, because the saves for ff7 and ff8 pc versions weren't changed, and the existing editors only needed to get updates for the new encryption method. You can also ask yourself "Would I bother to change something that works?", it would be a waste of money and time needed to implement and test a new method of saving game data.
The only reason I could think of that would necessitate doing that would be added functionality, but the game is completely unchanged, right?
tl;dr: No worries, this editor should work as soon as gjoerulv finds a way to get inside those files, edit them and reencrypt them.